Biopolym. Cell. 2003; 19(1):93-98.
Bioorganic Chemistry
The mechanism of interaction of monomethine cyanine dye Cyan 40 with dsDNA: computer modelling
1Yakovenko O. Ya., 1Golub A. G., 2Losytsky M. Yu., 1Bdzhola V. G., 1Yarmoluk S. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01033


The mechanism of interaction of cyanine dye Cyan 40 and DNA was studied by molecular modelling methods. The energy of interaction of the terminal parts of π-electrons clouds of aromatic heterocycles of DNA bases with Cyan 40 molecule was calculated by ab initio methods. We supposed that Cyan 40 interacted with dsDNA according to full-intercalation binding mode. Using combination of Amber, MM+, AMI, PM3 and ab initio calculation methods, the full-intercalation interaction of Cyan 40 with DNA was proved to be more favourable energetically than half-intercalation one. The series of the dye-DNA complex metastates were found, illustrating the hypothesis of three consequent stages of Cyan 40 interaction with DNA: (1) association of Cyan 40 with DNA minor groove, (2) interaction by half-intercalation mechanism, and (3) fixation of Cyan 40 between DNA bases pairs by the mechanism of full-intercalation.


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